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Genome analysis (Search for FMRP)

Welcome to Introduction to Bioinformatics Monday, 23 February 2009 Genome analysis / Viral Metagenomes. Genome analysis (Search for FMRP). (Flavors of Blast). Example with unknown sequence. Exam 1 retrospective (Problem 9 – coverage). Edwards & Rohwer – Viral Metagenomes.

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Genome analysis (Search for FMRP)

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  1. Welcome toIntroduction to BioinformaticsMonday, 23 February 2009Genome analysis / Viral Metagenomes • Genome analysis (Search for FMRP) (Flavors of Blast) • Example with unknown sequence • Exam 1 retrospective (Problem 9 – coverage) • Edwards & Rohwer – Viral Metagenomes • Mapping and Loops This demonstration is best viewed as a slide show,enabling you to simulate a session and make changes in cursor position more obvious.To do this, click Slide Show on the top tool bar, then View show.

  2. Search for FMRP

  3. Query Database Search for FMRP

  4. Query Database Search for FMRP

  5. Search for FMRP Query Database

  6. Search for mystery sequence

  7. Search for mystery sequence

  8. Search for any sequence

  9. Search for any sequence

  10. Search for FMRP

  11. Search for any sequence

  12. Search for any sequence Tobacco Mg chelatase (chlorophyll biosynthesis)100% identity, E-value = 0

  13. Search for any sequence Tobacco Mg chelatase (chlorophyll biosynthesis)40% identity, E-value = 3 x 10-4

  14. Search for any sequence Tobacco Mg chelatase (chlorophyll biosynthesis)100% identity, E-value = 0

  15. Search for any sequence Tobacco Mg chelatase (chlorophyll biosynthesis)100% identity, E-value = 0 Human melanocortin receptor Upstream region99% identity, E-value = 0 Meaning?

  16. Welcome toIntroduction to BioinformaticsMonday, 23 February 2009Genome analysis / Viral Metagenomes • Genome analysis (Search for FMRP) (Flavors of Blast) • Example with unknown sequence • Exam 1 retrospective (Problem 9 – coverage) • Edwards & Rohwer – Viral Metagenomes • Mapping and Loops

  17. Exam 1 retrospective

  18. Exam 1 retrospective

  19. Exam 1 retrospective

  20. Exam 1 retrospective SQ14.From figures given in the text and in Table 1, check the accuracy of each of the following…

  21. SQ14.From figures given in the text and in Table 1, check the accuracy of each of the following… Exam 1 retrospective

  22. Exam 1 retrospective

  23. Exam 1 retrospective

  24. Edwards & Rohwer (2005)What is metagenomics? SQ2. Genome sequencing vs metagenomic sequencing? What special challenges?

  25. FOR-EACH variable name Control section – Determines form of iteration Initialization section – Initializes loop variables before the loop begins Variable update section – Resets loop variables each iteration Body – Forms to be iterated Results section – Determines the result returned by the loop Final action – To be performed after last iteration Loops Workspace Undo | Redo Results

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